Hi Ming, I guess it's classical copy-paste error. This should work: ATOM 7 N AMSE A 81 7.102 12.859 3.614 0.90 20.31 N ATOM 8 CA AMSE A 81 8.211 12.620 2.560 0.90 23.63 C ATOM 9 CB AMSE A 81 9.571 13.306 2.815 0.90 26.76 C ATOM 10 CG AMSE A 81 10.379 13.756 1.572 0.90 33.90 C ATOM 11 SE AMSE A 81 9.481 15.049 0.267 0.90 61.25 SE ATOM 12 CE AMSE A 81 9.069 13.831 -1.266 0.90 54.62 C ATOM 13 C AMSE A 81 8.355 11.286 1.756 0.90 20.79 C ATOM 14 O AMSE A 81 7.994 11.272 0.577 0.90 21.96 O ATOM 7 N BMET A 81 7.102 12.859 3.614 0.10 20.31 N ATOM 8 CA BMET A 81 8.211 12.620 2.560 0.10 23.63 C ATOM 9 CB BMET A 81 9.571 13.306 2.815 0.10 26.76 C ATOM 10 CG BMET A 81 10.379 13.756 1.572 0.10 33.90 C ATOM 11 SD BMET A 81 9.481 15.049 0.267 0.10 61.25 S ATOM 12 CE BMET A 81 9.069 13.831 -1.266 0.10 54.62 C ATOM 13 C BMET A 81 8.355 11.286 1.756 0.10 20.79 C ATOM 14 O BMET A 81 7.994 11.272 0.577 0.10 21.96 O Pavel On 2/27/12 4:52 PM, Ming wrote:

Hi Pavel,

Here is the portion that keeps giving me errors. Thank you,

ATOM 7 N AMSE A 81 7.102 12.859 3.614 0.90 20.31 N ATOM 8 CA AMSE A 81 8.211 12.620 2.560 0.90 23.63 C ATOM 9 CB AMSE A 81 9.571 13.306 2.815 0.90 26.76 C ATOM 10 CG AMSE A 81 10.379 13.756 1.572 0.90 33.90 C ATOM 11 SE AMSE A 81 9.481 15.049 0.267 0.90 61.25 SE ATOM 12 CE AMSE A 81 9.069 13.831 -1.266 0.90 54.62 C ATOM 13 C AMSE A 81 8.355 11.286 1.756 0.90 20.79 C ATOM 14 O AMSE A 81 7.994 11.272 0.577 0.90 21.96 O ATOM 7 N BMET A 81 7.102 12.859 3.614 0.10 20.31 N ATOM 8 CA BMET A 81 8.211 12.620 2.560 0.10 23.63 C ATOM 9 CB BMET A 81 9.571 13.306 2.815 0.10 26.76 C ATOM 10 CG BMET A 81 10.379 13.756 1.572 0.10 33.90 C ATOM 11 SG BMET A 81 9.481 15.049 0.267 0.10 61.25 S ATOM 12 CE BMET A 81 9.069 13.831 -1.266 0.10 54.62 C ATOM 13 C BMET A 81 8.355 11.286 1.756 0.10 20.79 C ATOM 14 O BMET A 81 7.994 11.272 0.577 0.10 21.96 O

On Mon, Feb 27, 2012 at 5:12 PM, Pavel Afonine mailto:[email protected]> wrote:

Hi Ming,

can you send me the PDB file or its portion that still results in problem?

Pavel

On 2/27/12 1:47 PM, Ming wrote:

...

Hi all,

I was trying to refine a protein with phenix.refine. I want to refine AMSE and BMET with occupancies 0.5 and 0.5. What I did is modifying the pdb file by copy the coordinates of MET to MSE, and change the names to be AMSE and BMET, modifying the occupancy to be 0.5 and 0.5 for each one. Everything else like the atom names have been taken care of too. I used the readyset to make sure the pdb file is good. But phenix.refine keeps giving me error saying "numbers of atoms with unknown nonbonded energy type symbols ". Anyone here can help me with this please? Thanks in advance,